Molecule of the Month: Methyl-coenzyme M Reductase
Methanogens use sophisticated molecular tools to build methane
Pros and Cons of Methane Production
Tools of the Trade
Exploring the Structure
Methyl-Coenzyme M Reductase (PDB entries 1mro and 1hbm)
Two structures give a glimpse of the enzyme before and after its reaction. Before the reaction, the enzyme binds to two cofactors: coenzyme M, which carries the methyl group, and coenzyme B. The enzyme releases the methyl group as methane, and connects the two coenzymes together with a disulfide linkage. This unusual disulfide-linked molecule is then used by the cell to produce energy. PDB entry 1mro (on the left) shows the two coenzymes before the reaction (but doesn't include the methyl group--it would normally be attached to the smaller of the two, as shown with the dotted circle). PDB entry 1hbm (on the right) shows the linked molecule after the reaction. To explore these structures in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- Try using one of the 3D viewers at the PDB to view the amino acids that lock F430 in place, and position the two substrates.
- Nickel is relatively rare in enzymes, but is occasionally used in reactions that involve small gas molecules, such as in nickel-iron hydrogenase. Many bacteria have a system of proteins to gather nickel ions from their environment: try searching for "nickel transport" at the RCSB PDB to see some of these proteins.
Related PDB-101 Resources
- Browse Enzymes
- Browse Renewable Energy
- Browse Molecules and the Environment
- U. Ermler (2005) On the mechanism of methyl-coenzyme M reductase. Dalton Transactions 2005, 3451-3458.
- 1hbm: W. Grabarse, F. Mahlert, E. C. Duin, M. Goubeaud, S. Shima, R. K. Thauer, V. Lamzin & U. Ermler (2001) On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding. Journal of Molecular Biology 309, 315-330.
- 1mro: U. Ermler, W. Grabarse, S. Shima, M. Goubeaud & R. K. Thauer (1997) Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane production. Science 278, 1457-1462.
November 2014, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2014_11